Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170106_144547_715
Start time	2017-01-06 14:45:47
Run time	13:45:27.230
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZNF669, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF669/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170106_144547_715/task.callpeak_spp.spp_rep1.line_57.id_10 chipseq.bds.20170106_144547_715/task.callpeak_macs2.macs2_rep1.line_71.id_11 chipseq.bds.20170106_144547_715/task.callpeak_spp.spp_rep1_pr1.line_57.id_12 chipseq.bds.20170106_144547_715/task.callpeak_spp.spp_rep1_pr2.line_57.id_13 chipseq.bds.20170106_144547_715/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14 chipseq.bds.20170106_144547_715/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15 chipseq.bds.20170106_144547_715/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16 chipseq.bds.20170106_144547_715/task.callpeak_idr.idr2_rep1_pr.line_73.id_17 chipseq.bds.20170106_144547_715/task.callpeak_idr.idr_final_qc.line_219.id_20 chipseq.bds.20170106_144547_715/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21 chipseq.bds.20170106_144547_715/task.report.peak2hammock.line_412.id_22 chipseq.bds.20170106_144547_715/task.report.peak2hammock.line_412.id_23 chipseq.bds.20170106_144547_715/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_spp.spp_rep1.line_57.id_10
Name	spp rep1
Thread	thread_Root
PID	24304

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 14:45:53
End	2017-01-07 04:25:54
Elapsed	13:40:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
5297 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz 
opened /tmp/24304.1.q/RtmpJg4dtp/SRR1370889_1.nodup.tagAlign14f11e9df83f
done. read 16595469 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24304.1.q/RtmpJg4dtp/input15MReadsNSCLess1.05.50MSubsample.tagAlign14f112df0e4c
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1888793 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.194841837166575 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 50 
Phantom peak Correlation 0.1912932 
Normalized Strand cross-correlation coefficient (NSC) 1.031568 
Relative Strand cross-correlation Coefficient (RSC) 2.470119 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 3.009094  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.3323259  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000258 
Detected 475505 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3309	3489	.	0	.	32.3297592599516	-1	2.91539983521229	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3309	3489	.	0	.	32.3297592599516	-1	2.91539983521229	90

Num	2
ID	task.callpeak_macs2.macs2_rep1.line_71.id_11
Name	macs2 rep1
Thread	thread_Root
PID	24305

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 14:45:54
End	2017-01-06 15:43:33
Elapsed	00:57:38
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/signal/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/signal/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1 -o "SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/signal/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1 -o "SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/signal/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
30604 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:46:24: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 14:46:24: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:46:24: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:46:26:  1000000 
INFO  @ Fri, 06 Jan 2017 14:46:28:  2000000 
INFO  @ Fri, 06 Jan 2017 14:46:30:  3000000 
INFO  @ Fri, 06 Jan 2017 14:46:31:  4000000 
INFO  @ Fri, 06 Jan 2017 14:46:33:  5000000 
INFO  @ Fri, 06 Jan 2017 14:46:35:  6000000 
INFO  @ Fri, 06 Jan 2017 14:46:37:  7000000 
INFO  @ Fri, 06 Jan 2017 14:46:39:  8000000 
INFO  @ Fri, 06 Jan 2017 14:46:41:  9000000 
INFO  @ Fri, 06 Jan 2017 14:46:42:  10000000 
INFO  @ Fri, 06 Jan 2017 14:46:44:  11000000 
INFO  @ Fri, 06 Jan 2017 14:46:46:  12000000 
INFO  @ Fri, 06 Jan 2017 14:46:48:  13000000 
INFO  @ Fri, 06 Jan 2017 14:46:50:  14000000 
INFO  @ Fri, 06 Jan 2017 14:46:52:  15000000 
INFO  @ Fri, 06 Jan 2017 14:46:53:  16000000 
INFO  @ Fri, 06 Jan 2017 14:46:55: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:46:57:  1000000 
INFO  @ Fri, 06 Jan 2017 14:46:58:  2000000 
INFO  @ Fri, 06 Jan 2017 14:47:00:  3000000 
INFO  @ Fri, 06 Jan 2017 14:47:02:  4000000 
INFO  @ Fri, 06 Jan 2017 14:47:04:  5000000 
INFO  @ Fri, 06 Jan 2017 14:47:06:  6000000 
INFO  @ Fri, 06 Jan 2017 14:47:08:  7000000 
INFO  @ Fri, 06 Jan 2017 14:47:10:  8000000 
INFO  @ Fri, 06 Jan 2017 14:47:11:  9000000 
INFO  @ Fri, 06 Jan 2017 14:47:13:  10000000 
INFO  @ Fri, 06 Jan 2017 14:47:15:  11000000 
INFO  @ Fri, 06 Jan 2017 14:47:17:  12000000 
INFO  @ Fri, 06 Jan 2017 14:47:19:  13000000 
INFO  @ Fri, 06 Jan 2017 14:47:20:  14000000 
INFO  @ Fri, 06 Jan 2017 14:47:22:  15000000 
INFO  @ Fri, 06 Jan 2017 14:47:24:  16000000 
INFO  @ Fri, 06 Jan 2017 14:47:26:  17000000 
INFO  @ Fri, 06 Jan 2017 14:47:28:  18000000 
INFO  @ Fri, 06 Jan 2017 14:47:30:  19000000 
INFO  @ Fri, 06 Jan 2017 14:47:32:  20000000 
INFO  @ Fri, 06 Jan 2017 14:47:33:  21000000 
INFO  @ Fri, 06 Jan 2017 14:47:35:  22000000 
INFO  @ Fri, 06 Jan 2017 14:47:37:  23000000 
INFO  @ Fri, 06 Jan 2017 14:47:39:  24000000 
INFO  @ Fri, 06 Jan 2017 14:47:41:  25000000 
INFO  @ Fri, 06 Jan 2017 14:47:42:  26000000 
INFO  @ Fri, 06 Jan 2017 14:47:44:  27000000 
INFO  @ Fri, 06 Jan 2017 14:47:46:  28000000 
INFO  @ Fri, 06 Jan 2017 14:47:48:  29000000 
INFO  @ Fri, 06 Jan 2017 14:47:50:  30000000 
INFO  @ Fri, 06 Jan 2017 14:47:52:  31000000 
INFO  @ Fri, 06 Jan 2017 14:47:53:  32000000 
INFO  @ Fri, 06 Jan 2017 14:47:55:  33000000 
INFO  @ Fri, 06 Jan 2017 14:47:57:  34000000 
INFO  @ Fri, 06 Jan 2017 14:47:59:  35000000 
INFO  @ Fri, 06 Jan 2017 14:48:01:  36000000 
INFO  @ Fri, 06 Jan 2017 14:48:03:  37000000 
INFO  @ Fri, 06 Jan 2017 14:48:04:  38000000 
INFO  @ Fri, 06 Jan 2017 14:48:06:  39000000 
INFO  @ Fri, 06 Jan 2017 14:48:08:  40000000 
INFO  @ Fri, 06 Jan 2017 14:48:10:  41000000 
INFO  @ Fri, 06 Jan 2017 14:48:12:  42000000 
INFO  @ Fri, 06 Jan 2017 14:48:14:  43000000 
INFO  @ Fri, 06 Jan 2017 14:48:15:  44000000 
INFO  @ Fri, 06 Jan 2017 14:48:17:  45000000 
INFO  @ Fri, 06 Jan 2017 14:48:19:  46000000 
INFO  @ Fri, 06 Jan 2017 14:48:21:  47000000 
INFO  @ Fri, 06 Jan 2017 14:48:23:  48000000 
INFO  @ Fri, 06 Jan 2017 14:48:24:  49000000 
INFO  @ Fri, 06 Jan 2017 14:48:26:  50000000 
INFO  @ Fri, 06 Jan 2017 14:48:28: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:48:28: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:48:28: #1  total tags in treatment: 16595469 
INFO  @ Fri, 06 Jan 2017 14:48:28: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:48:28: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:48:28: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:48:28: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:48:28: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:48:28: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:48:28: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:48:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:51:09: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:51:09: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:51:09: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:51:09: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:51:09: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 14:56:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 14:56:22: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 14:56:22: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 14:56:23: Done! 
INFO  @ Fri, 06 Jan 2017 14:56:25: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 14:56:25: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:56:25: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:56:27:  1000000 
INFO  @ Fri, 06 Jan 2017 14:56:29:  2000000 
INFO  @ Fri, 06 Jan 2017 14:56:30:  3000000 
INFO  @ Fri, 06 Jan 2017 14:56:32:  4000000 
INFO  @ Fri, 06 Jan 2017 14:56:33:  5000000 
INFO  @ Fri, 06 Jan 2017 14:56:35:  6000000 
INFO  @ Fri, 06 Jan 2017 14:56:36:  7000000 
INFO  @ Fri, 06 Jan 2017 14:56:38:  8000000 
INFO  @ Fri, 06 Jan 2017 14:56:39:  9000000 
INFO  @ Fri, 06 Jan 2017 14:56:41:  10000000 
INFO  @ Fri, 06 Jan 2017 14:56:42:  11000000 
INFO  @ Fri, 06 Jan 2017 14:56:44:  12000000 
INFO  @ Fri, 06 Jan 2017 14:56:45:  13000000 
INFO  @ Fri, 06 Jan 2017 14:56:47:  14000000 
INFO  @ Fri, 06 Jan 2017 14:56:48:  15000000 
INFO  @ Fri, 06 Jan 2017 14:56:50:  16000000 
INFO  @ Fri, 06 Jan 2017 14:56:51: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:56:53:  1000000 
INFO  @ Fri, 06 Jan 2017 14:56:54:  2000000 
INFO  @ Fri, 06 Jan 2017 14:56:56:  3000000 
INFO  @ Fri, 06 Jan 2017 14:56:58:  4000000 
INFO  @ Fri, 06 Jan 2017 14:56:59:  5000000 
INFO  @ Fri, 06 Jan 2017 14:57:01:  6000000 
INFO  @ Fri, 06 Jan 2017 14:57:02:  7000000 
INFO  @ Fri, 06 Jan 2017 14:57:04:  8000000 
INFO  @ Fri, 06 Jan 2017 14:57:05:  9000000 
INFO  @ Fri, 06 Jan 2017 14:57:07:  10000000 
INFO  @ Fri, 06 Jan 2017 14:57:08:  11000000 
INFO  @ Fri, 06 Jan 2017 14:57:10:  12000000 
INFO  @ Fri, 06 Jan 2017 14:57:11:  13000000 
INFO  @ Fri, 06 Jan 2017 14:57:13:  14000000 
INFO  @ Fri, 06 Jan 2017 14:57:15:  15000000 
INFO  @ Fri, 06 Jan 2017 14:57:16:  16000000 
INFO  @ Fri, 06 Jan 2017 14:57:18:  17000000 
INFO  @ Fri, 06 Jan 2017 14:57:19:  18000000 
INFO  @ Fri, 06 Jan 2017 14:57:21:  19000000 
INFO  @ Fri, 06 Jan 2017 14:57:22:  20000000 
INFO  @ Fri, 06 Jan 2017 14:57:24:  21000000 
INFO  @ Fri, 06 Jan 2017 14:57:25:  22000000 
INFO  @ Fri, 06 Jan 2017 14:57:27:  23000000 
INFO  @ Fri, 06 Jan 2017 14:57:28:  24000000 
INFO  @ Fri, 06 Jan 2017 14:57:30:  25000000 
INFO  @ Fri, 06 Jan 2017 14:57:31:  26000000 
INFO  @ Fri, 06 Jan 2017 14:57:33:  27000000 
INFO  @ Fri, 06 Jan 2017 14:57:34:  28000000 
INFO  @ Fri, 06 Jan 2017 14:57:36:  29000000 
INFO  @ Fri, 06 Jan 2017 14:57:38:  30000000 
INFO  @ Fri, 06 Jan 2017 14:57:39:  31000000 
INFO  @ Fri, 06 Jan 2017 14:57:41:  32000000 
INFO  @ Fri, 06 Jan 2017 14:57:42:  33000000 
INFO  @ Fri, 06 Jan 2017 14:57:44:  34000000 
INFO  @ Fri, 06 Jan 2017 14:57:45:  35000000 
INFO  @ Fri, 06 Jan 2017 14:57:47:  36000000 
INFO  @ Fri, 06 Jan 2017 14:57:48:  37000000 
INFO  @ Fri, 06 Jan 2017 14:57:50:  38000000 
INFO  @ Fri, 06 Jan 2017 14:57:52:  39000000 
INFO  @ Fri, 06 Jan 2017 14:57:53:  40000000 
INFO  @ Fri, 06 Jan 2017 14:57:55:  41000000 
INFO  @ Fri, 06 Jan 2017 14:57:56:  42000000 
INFO  @ Fri, 06 Jan 2017 14:57:58:  43000000 
INFO  @ Fri, 06 Jan 2017 14:57:59:  44000000 
INFO  @ Fri, 06 Jan 2017 14:58:01:  45000000 
INFO  @ Fri, 06 Jan 2017 14:58:02:  46000000 
INFO  @ Fri, 06 Jan 2017 14:58:04:  47000000 
INFO  @ Fri, 06 Jan 2017 14:58:05:  48000000 
INFO  @ Fri, 06 Jan 2017 14:58:07:  49000000 
INFO  @ Fri, 06 Jan 2017 14:58:08:  50000000 
INFO  @ Fri, 06 Jan 2017 14:58:10: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:58:10: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:58:10: #1  total tags in treatment: 16595469 
INFO  @ Fri, 06 Jan 2017 14:58:10: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:58:10: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:58:10: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:58:10: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:58:10: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:58:10: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:58:10: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 14:58:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:00:45: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:03:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:03:18: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:03:23: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:03:28: Done! 
INFO  @ Fri, 06 Jan 2017 15:03:46: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:04:22: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:06:17: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:07:09: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Fri, 06 Jan 2017 15:12:42: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:15:44: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_FE.bdg'! 
INFO  @ Fri, 06 Jan 2017 15:22:23: Read and build treatment bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:23:01: Read and build control bedGraph... 
INFO  @ Fri, 06 Jan 2017 15:25:01: Build scoreTrackII... 
INFO  @ Fri, 06 Jan 2017 15:25:51: Values in your input bedGraph files will be multiplied by 16.595469 ... 
INFO  @ Fri, 06 Jan 2017 15:31:21: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Fri, 06 Jan 2017 15:32:03: Write bedGraph of scores... 
INFO  @ Fri, 06 Jan 2017 15:35:21: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_ppois.bdg'!

Num	3
ID	task.callpeak_spp.spp_rep1_pr1.line_57.id_12
Name	spp rep1-pr1
Thread	thread_Root
PID	24306

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 14:45:55
End	2017-01-07 03:03:48
Elapsed	12:17:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
5430 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz 
opened /tmp/24306.1.q/RtmpaFOudI/SRR1370889_1.nodup.pr1.tagAlign157d1ddd828d
done. read 8297735 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24306.1.q/RtmpaFOudI/input15MReadsNSCLess1.05.50MSubsample.tagAlign157d40f81368
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.1049825 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.108266905508462 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 50 
Phantom peak Correlation 0.1063918 
Normalized Strand cross-correlation coefficient (NSC) 1.031285 
Relative Strand cross-correlation Coefficient (RSC) 2.330433 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 6.017759  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1661748  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000041 
Detected 159858 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2265	2445	.	0	.	19.9429920025622	-1	3.18760654130545	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2265	2445	.	0	.	19.9429920025622	-1	3.18760654130545	90

Num	4
ID	task.callpeak_spp.spp_rep1_pr2.line_57.id_13
Name	spp rep1-pr2
Thread	thread_Root
PID	24307

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 14:45:56
End	2017-01-07 03:23:50
Elapsed	12:37:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf
Dependencies

 
# SYS command. line 59

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 62

 if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 66

 Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz \
			-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2 -speak=145 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 72

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz

# SYS command. line 74

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pdf

# SYS command. line 77

 if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz; fi

# SYS command. line 80

 if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi

# SYS command. line 82

 if [[ true == "true" ]]; then \
			bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.regionPeak.gz; \
		fi

# SYS command. line 86

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
30791 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz 
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 145 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 1 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2 
narrowPeak output file name: NA 
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_VS_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.ccscore 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz 
opened /tmp/24307.1.q/RtmpeIYqk4/SRR1370889_1.nodup.pr2.tagAlign78966ca8790e
done. read 8297734 fragments
ChIP data read length 51 
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz 
opened /tmp/24307.1.q/RtmpeIYqk4/input15MReadsNSCLess1.05.50MSubsample.tagAlign7896188942a9
done. read 50000000 fragments
Control data read length 68 
Calculating peak characteristics
Minimum cross-correlation value 0.104786 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.108057614408194 
Top 3 estimates for fragment length 145 
Window half size 180 
Phantom peak location 50 
Phantom peak Correlation 0.1061702 
Normalized Strand cross-correlation coefficient (NSC) 1.031222 
Relative Strand cross-correlation Coefficient (RSC) 2.363474 
Phantom Peak Quality Tag 2 
null device 
          1 
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 6.01774  excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 0.1661753  excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00004 
Detected 159316 peaks 

 
--------------------Stderr--------------------
Loading required package: caTools
There were 50 or more warnings (use warnings() to see the first 50)
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2551	2731	.	0	.	11.5677656620501	-1	3.31844391275814	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	2551	2731	.	0	.	11.5677656620501	-1	3.31844391275814	90

Num	5
ID	task.callpeak_macs2.macs2_rep1_pr1.line_71.id_14
Name	macs2 rep1-pr1
Thread	thread_Root
PID	24308

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 14:45:57
End	2017-01-06 15:09:22
Elapsed	00:23:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
5568 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 14:48:53: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 14:48:53: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 14:48:53: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 14:48:55:  1000000 
INFO  @ Fri, 06 Jan 2017 14:48:57:  2000000 
INFO  @ Fri, 06 Jan 2017 14:48:58:  3000000 
INFO  @ Fri, 06 Jan 2017 14:49:00:  4000000 
INFO  @ Fri, 06 Jan 2017 14:49:02:  5000000 
INFO  @ Fri, 06 Jan 2017 14:49:04:  6000000 
INFO  @ Fri, 06 Jan 2017 14:49:06:  7000000 
INFO  @ Fri, 06 Jan 2017 14:49:08:  8000000 
INFO  @ Fri, 06 Jan 2017 14:49:10: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 14:49:12:  1000000 
INFO  @ Fri, 06 Jan 2017 14:49:14:  2000000 
INFO  @ Fri, 06 Jan 2017 14:49:16:  3000000 
INFO  @ Fri, 06 Jan 2017 14:49:19:  4000000 
INFO  @ Fri, 06 Jan 2017 14:49:21:  5000000 
INFO  @ Fri, 06 Jan 2017 14:49:23:  6000000 
INFO  @ Fri, 06 Jan 2017 14:49:25:  7000000 
INFO  @ Fri, 06 Jan 2017 14:49:28:  8000000 
INFO  @ Fri, 06 Jan 2017 14:49:29:  9000000 
INFO  @ Fri, 06 Jan 2017 14:49:31:  10000000 
INFO  @ Fri, 06 Jan 2017 14:49:33:  11000000 
INFO  @ Fri, 06 Jan 2017 14:49:35:  12000000 
INFO  @ Fri, 06 Jan 2017 14:49:37:  13000000 
INFO  @ Fri, 06 Jan 2017 14:49:38:  14000000 
INFO  @ Fri, 06 Jan 2017 14:49:40:  15000000 
INFO  @ Fri, 06 Jan 2017 14:49:41:  16000000 
INFO  @ Fri, 06 Jan 2017 14:49:43:  17000000 
INFO  @ Fri, 06 Jan 2017 14:49:45:  18000000 
INFO  @ Fri, 06 Jan 2017 14:49:46:  19000000 
INFO  @ Fri, 06 Jan 2017 14:49:48:  20000000 
INFO  @ Fri, 06 Jan 2017 14:49:49:  21000000 
INFO  @ Fri, 06 Jan 2017 14:49:51:  22000000 
INFO  @ Fri, 06 Jan 2017 14:49:52:  23000000 
INFO  @ Fri, 06 Jan 2017 14:49:54:  24000000 
INFO  @ Fri, 06 Jan 2017 14:49:55:  25000000 
INFO  @ Fri, 06 Jan 2017 14:49:57:  26000000 
INFO  @ Fri, 06 Jan 2017 14:49:58:  27000000 
INFO  @ Fri, 06 Jan 2017 14:50:00:  28000000 
INFO  @ Fri, 06 Jan 2017 14:50:01:  29000000 
INFO  @ Fri, 06 Jan 2017 14:50:03:  30000000 
INFO  @ Fri, 06 Jan 2017 14:50:04:  31000000 
INFO  @ Fri, 06 Jan 2017 14:50:06:  32000000 
INFO  @ Fri, 06 Jan 2017 14:50:08:  33000000 
INFO  @ Fri, 06 Jan 2017 14:50:09:  34000000 
INFO  @ Fri, 06 Jan 2017 14:50:11:  35000000 
INFO  @ Fri, 06 Jan 2017 14:50:12:  36000000 
INFO  @ Fri, 06 Jan 2017 14:50:14:  37000000 
INFO  @ Fri, 06 Jan 2017 14:50:15:  38000000 
INFO  @ Fri, 06 Jan 2017 14:50:17:  39000000 
INFO  @ Fri, 06 Jan 2017 14:50:18:  40000000 
INFO  @ Fri, 06 Jan 2017 14:50:20:  41000000 
INFO  @ Fri, 06 Jan 2017 14:50:21:  42000000 
INFO  @ Fri, 06 Jan 2017 14:50:23:  43000000 
INFO  @ Fri, 06 Jan 2017 14:50:25:  44000000 
INFO  @ Fri, 06 Jan 2017 14:50:26:  45000000 
INFO  @ Fri, 06 Jan 2017 14:50:28:  46000000 
INFO  @ Fri, 06 Jan 2017 14:50:30:  47000000 
INFO  @ Fri, 06 Jan 2017 14:50:31:  48000000 
INFO  @ Fri, 06 Jan 2017 14:50:33:  49000000 
INFO  @ Fri, 06 Jan 2017 14:50:34:  50000000 
INFO  @ Fri, 06 Jan 2017 14:50:36: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 14:50:36: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 14:50:36: #1  total tags in treatment: 8297735 
INFO  @ Fri, 06 Jan 2017 14:50:36: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 14:50:36: #1 finished! 
INFO  @ Fri, 06 Jan 2017 14:50:36: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 14:50:36: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 14:50:36: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 14:50:36: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 14:50:36: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 14:50:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 14:55:00: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 14:55:00: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:00: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 14:55:00: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 14:55:00: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:00:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:00:10: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:00:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:00:11: Done! 
INFO  @ Fri, 06 Jan 2017 15:00:14: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 15:00:14: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:00:14: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:00:17:  1000000 
INFO  @ Fri, 06 Jan 2017 15:00:19:  2000000 
INFO  @ Fri, 06 Jan 2017 15:00:20:  3000000 
INFO  @ Fri, 06 Jan 2017 15:00:22:  4000000 
INFO  @ Fri, 06 Jan 2017 15:00:24:  5000000 
INFO  @ Fri, 06 Jan 2017 15:00:26:  6000000 
INFO  @ Fri, 06 Jan 2017 15:00:28:  7000000 
INFO  @ Fri, 06 Jan 2017 15:00:30:  8000000 
INFO  @ Fri, 06 Jan 2017 15:00:31: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:00:33:  1000000 
INFO  @ Fri, 06 Jan 2017 15:00:35:  2000000 
INFO  @ Fri, 06 Jan 2017 15:00:37:  3000000 
INFO  @ Fri, 06 Jan 2017 15:00:40:  4000000 
INFO  @ Fri, 06 Jan 2017 15:00:42:  5000000 
INFO  @ Fri, 06 Jan 2017 15:00:44:  6000000 
INFO  @ Fri, 06 Jan 2017 15:00:46:  7000000 
INFO  @ Fri, 06 Jan 2017 15:00:48:  8000000 
INFO  @ Fri, 06 Jan 2017 15:00:50:  9000000 
INFO  @ Fri, 06 Jan 2017 15:00:51:  10000000 
INFO  @ Fri, 06 Jan 2017 15:00:54:  11000000 
INFO  @ Fri, 06 Jan 2017 15:00:56:  12000000 
INFO  @ Fri, 06 Jan 2017 15:00:58:  13000000 
INFO  @ Fri, 06 Jan 2017 15:01:00:  14000000 
INFO  @ Fri, 06 Jan 2017 15:01:03:  15000000 
INFO  @ Fri, 06 Jan 2017 15:01:04:  16000000 
INFO  @ Fri, 06 Jan 2017 15:01:06:  17000000 
INFO  @ Fri, 06 Jan 2017 15:01:08:  18000000 
INFO  @ Fri, 06 Jan 2017 15:01:10:  19000000 
INFO  @ Fri, 06 Jan 2017 15:01:12:  20000000 
INFO  @ Fri, 06 Jan 2017 15:01:14:  21000000 
INFO  @ Fri, 06 Jan 2017 15:01:16:  22000000 
INFO  @ Fri, 06 Jan 2017 15:01:18:  23000000 
INFO  @ Fri, 06 Jan 2017 15:01:20:  24000000 
INFO  @ Fri, 06 Jan 2017 15:01:22:  25000000 
INFO  @ Fri, 06 Jan 2017 15:01:24:  26000000 
INFO  @ Fri, 06 Jan 2017 15:01:26:  27000000 
INFO  @ Fri, 06 Jan 2017 15:01:28:  28000000 
INFO  @ Fri, 06 Jan 2017 15:01:30:  29000000 
INFO  @ Fri, 06 Jan 2017 15:01:32:  30000000 
INFO  @ Fri, 06 Jan 2017 15:01:34:  31000000 
INFO  @ Fri, 06 Jan 2017 15:01:36:  32000000 
INFO  @ Fri, 06 Jan 2017 15:01:38:  33000000 
INFO  @ Fri, 06 Jan 2017 15:01:40:  34000000 
INFO  @ Fri, 06 Jan 2017 15:01:42:  35000000 
INFO  @ Fri, 06 Jan 2017 15:01:44:  36000000 
INFO  @ Fri, 06 Jan 2017 15:01:45:  37000000 
INFO  @ Fri, 06 Jan 2017 15:01:47:  38000000 
INFO  @ Fri, 06 Jan 2017 15:01:49:  39000000 
INFO  @ Fri, 06 Jan 2017 15:01:51:  40000000 
INFO  @ Fri, 06 Jan 2017 15:01:53:  41000000 
INFO  @ Fri, 06 Jan 2017 15:01:55:  42000000 
INFO  @ Fri, 06 Jan 2017 15:01:57:  43000000 
INFO  @ Fri, 06 Jan 2017 15:01:58:  44000000 
INFO  @ Fri, 06 Jan 2017 15:02:00:  45000000 
INFO  @ Fri, 06 Jan 2017 15:02:02:  46000000 
INFO  @ Fri, 06 Jan 2017 15:02:04:  47000000 
INFO  @ Fri, 06 Jan 2017 15:02:05:  48000000 
INFO  @ Fri, 06 Jan 2017 15:02:07:  49000000 
INFO  @ Fri, 06 Jan 2017 15:02:09:  50000000 
INFO  @ Fri, 06 Jan 2017 15:02:10: #1 tag size is determined as 51 bps 
INFO  @ Fri, 06 Jan 2017 15:02:10: #1 tag size = 51 
INFO  @ Fri, 06 Jan 2017 15:02:10: #1  total tags in treatment: 8297735 
INFO  @ Fri, 06 Jan 2017 15:02:10: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:02:10: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:02:10: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:02:10: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:02:10: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:02:10: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:02:10: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:02:10: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:05:17: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:08:42: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:08:51: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:08:59: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:09:05: Done!

Num	6
ID	task.callpeak_macs2.macs2_rep1_pr2.line_71.id_15
Name	macs2 rep1-pr2
Thread	thread_Root
PID	24319

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-06 15:09:24
End	2017-01-06 15:46:01
Elapsed	00:36:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
8568 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Fri, 06 Jan 2017 15:28:40: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 145 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Fri, 06 Jan 2017 15:28:40: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:28:40: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:28:42:  1000000 
INFO  @ Fri, 06 Jan 2017 15:28:44:  2000000 
INFO  @ Fri, 06 Jan 2017 15:28:45:  3000000 
INFO  @ Fri, 06 Jan 2017 15:28:47:  4000000 
INFO  @ Fri, 06 Jan 2017 15:28:49:  5000000 
INFO  @ Fri, 06 Jan 2017 15:28:50:  6000000 
INFO  @ Fri, 06 Jan 2017 15:28:52:  7000000 
INFO  @ Fri, 06 Jan 2017 15:28:54:  8000000 
INFO  @ Fri, 06 Jan 2017 15:28:55: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:28:56:  1000000 
INFO  @ Fri, 06 Jan 2017 15:28:58:  2000000 
INFO  @ Fri, 06 Jan 2017 15:29:00:  3000000 
INFO  @ Fri, 06 Jan 2017 15:29:01:  4000000 
INFO  @ Fri, 06 Jan 2017 15:29:03:  5000000 
INFO  @ Fri, 06 Jan 2017 15:29:05:  6000000 
INFO  @ Fri, 06 Jan 2017 15:29:06:  7000000 
INFO  @ Fri, 06 Jan 2017 15:29:08:  8000000 
INFO  @ Fri, 06 Jan 2017 15:29:10:  9000000 
INFO  @ Fri, 06 Jan 2017 15:29:12:  10000000 
INFO  @ Fri, 06 Jan 2017 15:29:14:  11000000 
INFO  @ Fri, 06 Jan 2017 15:29:16:  12000000 
INFO  @ Fri, 06 Jan 2017 15:29:17:  13000000 
INFO  @ Fri, 06 Jan 2017 15:29:19:  14000000 
INFO  @ Fri, 06 Jan 2017 15:29:21:  15000000 
INFO  @ Fri, 06 Jan 2017 15:29:22:  16000000 
INFO  @ Fri, 06 Jan 2017 15:29:24:  17000000 
INFO  @ Fri, 06 Jan 2017 15:29:26:  18000000 
INFO  @ Fri, 06 Jan 2017 15:29:28:  19000000 
INFO  @ Fri, 06 Jan 2017 15:29:30:  20000000 
INFO  @ Fri, 06 Jan 2017 15:29:31:  21000000 
INFO  @ Fri, 06 Jan 2017 15:29:33:  22000000 
INFO  @ Fri, 06 Jan 2017 15:29:35:  23000000 
INFO  @ Fri, 06 Jan 2017 15:29:36:  24000000 
INFO  @ Fri, 06 Jan 2017 15:29:38:  25000000 
INFO  @ Fri, 06 Jan 2017 15:29:40:  26000000 
INFO  @ Fri, 06 Jan 2017 15:29:41:  27000000 
INFO  @ Fri, 06 Jan 2017 15:29:43:  28000000 
INFO  @ Fri, 06 Jan 2017 15:29:44:  29000000 
INFO  @ Fri, 06 Jan 2017 15:29:46:  30000000 
INFO  @ Fri, 06 Jan 2017 15:29:48:  31000000 
INFO  @ Fri, 06 Jan 2017 15:29:49:  32000000 
INFO  @ Fri, 06 Jan 2017 15:29:51:  33000000 
INFO  @ Fri, 06 Jan 2017 15:29:52:  34000000 
INFO  @ Fri, 06 Jan 2017 15:29:54:  35000000 
INFO  @ Fri, 06 Jan 2017 15:29:55:  36000000 
INFO  @ Fri, 06 Jan 2017 15:29:57:  37000000 
INFO  @ Fri, 06 Jan 2017 15:29:59:  38000000 
INFO  @ Fri, 06 Jan 2017 15:30:00:  39000000 
INFO  @ Fri, 06 Jan 2017 15:30:02:  40000000 
INFO  @ Fri, 06 Jan 2017 15:30:04:  41000000 
INFO  @ Fri, 06 Jan 2017 15:30:05:  42000000 
INFO  @ Fri, 06 Jan 2017 15:30:07:  43000000 
INFO  @ Fri, 06 Jan 2017 15:30:08:  44000000 
INFO  @ Fri, 06 Jan 2017 15:30:10:  45000000 
INFO  @ Fri, 06 Jan 2017 15:30:12:  46000000 
INFO  @ Fri, 06 Jan 2017 15:30:13:  47000000 
INFO  @ Fri, 06 Jan 2017 15:30:15:  48000000 
INFO  @ Fri, 06 Jan 2017 15:30:16:  49000000 
INFO  @ Fri, 06 Jan 2017 15:30:18:  50000000 
INFO  @ Fri, 06 Jan 2017 15:30:20: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:30:20: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:30:20: #1  total tags in treatment: 8297734 
INFO  @ Fri, 06 Jan 2017 15:30:20: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:30:20: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:30:20: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:30:20: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:30:20: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:30:20: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:30:20: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Fri, 06 Jan 2017 15:30:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:33:23: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Fri, 06 Jan 2017 15:33:23: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_treat_pileup.bdg 
INFO  @ Fri, 06 Jan 2017 15:33:23: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_control_lambda.bdg 
INFO  @ Fri, 06 Jan 2017 15:33:23: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Fri, 06 Jan 2017 15:33:23: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:38:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:38:09: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.narrowPeak 
INFO  @ Fri, 06 Jan 2017 15:38:09: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_summits.bed 
INFO  @ Fri, 06 Jan 2017 15:38:10: Done! 
INFO  @ Fri, 06 Jan 2017 15:38:12: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 145 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Fri, 06 Jan 2017 15:38:12: #1 read tag files... 
INFO  @ Fri, 06 Jan 2017 15:38:12: #1 read treatment tags... 
INFO  @ Fri, 06 Jan 2017 15:38:14:  1000000 
INFO  @ Fri, 06 Jan 2017 15:38:16:  2000000 
INFO  @ Fri, 06 Jan 2017 15:38:17:  3000000 
INFO  @ Fri, 06 Jan 2017 15:38:19:  4000000 
INFO  @ Fri, 06 Jan 2017 15:38:21:  5000000 
INFO  @ Fri, 06 Jan 2017 15:38:22:  6000000 
INFO  @ Fri, 06 Jan 2017 15:38:24:  7000000 
INFO  @ Fri, 06 Jan 2017 15:38:26:  8000000 
INFO  @ Fri, 06 Jan 2017 15:38:27: #1.2 read input tags... 
INFO  @ Fri, 06 Jan 2017 15:38:28:  1000000 
INFO  @ Fri, 06 Jan 2017 15:38:30:  2000000 
INFO  @ Fri, 06 Jan 2017 15:38:32:  3000000 
INFO  @ Fri, 06 Jan 2017 15:38:33:  4000000 
INFO  @ Fri, 06 Jan 2017 15:38:35:  5000000 
INFO  @ Fri, 06 Jan 2017 15:38:36:  6000000 
INFO  @ Fri, 06 Jan 2017 15:38:38:  7000000 
INFO  @ Fri, 06 Jan 2017 15:38:39:  8000000 
INFO  @ Fri, 06 Jan 2017 15:38:41:  9000000 
INFO  @ Fri, 06 Jan 2017 15:38:43:  10000000 
INFO  @ Fri, 06 Jan 2017 15:38:44:  11000000 
INFO  @ Fri, 06 Jan 2017 15:38:46:  12000000 
INFO  @ Fri, 06 Jan 2017 15:38:47:  13000000 
INFO  @ Fri, 06 Jan 2017 15:38:49:  14000000 
INFO  @ Fri, 06 Jan 2017 15:38:50:  15000000 
INFO  @ Fri, 06 Jan 2017 15:38:52:  16000000 
INFO  @ Fri, 06 Jan 2017 15:38:53:  17000000 
INFO  @ Fri, 06 Jan 2017 15:38:55:  18000000 
INFO  @ Fri, 06 Jan 2017 15:38:57:  19000000 
INFO  @ Fri, 06 Jan 2017 15:38:58:  20000000 
INFO  @ Fri, 06 Jan 2017 15:39:00:  21000000 
INFO  @ Fri, 06 Jan 2017 15:39:01:  22000000 
INFO  @ Fri, 06 Jan 2017 15:39:03:  23000000 
INFO  @ Fri, 06 Jan 2017 15:39:04:  24000000 
INFO  @ Fri, 06 Jan 2017 15:39:06:  25000000 
INFO  @ Fri, 06 Jan 2017 15:39:08:  26000000 
INFO  @ Fri, 06 Jan 2017 15:39:09:  27000000 
INFO  @ Fri, 06 Jan 2017 15:39:11:  28000000 
INFO  @ Fri, 06 Jan 2017 15:39:12:  29000000 
INFO  @ Fri, 06 Jan 2017 15:39:14:  30000000 
INFO  @ Fri, 06 Jan 2017 15:39:15:  31000000 
INFO  @ Fri, 06 Jan 2017 15:39:17:  32000000 
INFO  @ Fri, 06 Jan 2017 15:39:18:  33000000 
INFO  @ Fri, 06 Jan 2017 15:39:20:  34000000 
INFO  @ Fri, 06 Jan 2017 15:39:22:  35000000 
INFO  @ Fri, 06 Jan 2017 15:39:23:  36000000 
INFO  @ Fri, 06 Jan 2017 15:39:25:  37000000 
INFO  @ Fri, 06 Jan 2017 15:39:27:  38000000 
INFO  @ Fri, 06 Jan 2017 15:39:28:  39000000 
INFO  @ Fri, 06 Jan 2017 15:39:30:  40000000 
INFO  @ Fri, 06 Jan 2017 15:39:31:  41000000 
INFO  @ Fri, 06 Jan 2017 15:39:33:  42000000 
INFO  @ Fri, 06 Jan 2017 15:39:35:  43000000 
INFO  @ Fri, 06 Jan 2017 15:39:37:  44000000 
INFO  @ Fri, 06 Jan 2017 15:39:38:  45000000 
INFO  @ Fri, 06 Jan 2017 15:39:40:  46000000 
INFO  @ Fri, 06 Jan 2017 15:39:42:  47000000 
INFO  @ Fri, 06 Jan 2017 15:39:44:  48000000 
INFO  @ Fri, 06 Jan 2017 15:39:45:  49000000 
INFO  @ Fri, 06 Jan 2017 15:39:47:  50000000 
INFO  @ Fri, 06 Jan 2017 15:39:49: #1 tag size is determined as 50 bps 
INFO  @ Fri, 06 Jan 2017 15:39:49: #1 tag size = 50 
INFO  @ Fri, 06 Jan 2017 15:39:49: #1  total tags in treatment: 8297734 
INFO  @ Fri, 06 Jan 2017 15:39:49: #1  total tags in control: 50000000 
INFO  @ Fri, 06 Jan 2017 15:39:49: #1 finished! 
INFO  @ Fri, 06 Jan 2017 15:39:49: #2 Build Peak Model... 
INFO  @ Fri, 06 Jan 2017 15:39:49: #2 Skipped... 
INFO  @ Fri, 06 Jan 2017 15:39:49: #2 Use 145 as fragment length 
INFO  @ Fri, 06 Jan 2017 15:39:49: #3 Call peaks... 
INFO  @ Fri, 06 Jan 2017 15:39:49: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Fri, 06 Jan 2017 15:39:49: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 06 Jan 2017 15:42:45: #3 Call peaks for each chromosome... 
INFO  @ Fri, 06 Jan 2017 15:45:26: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.xls 
INFO  @ Fri, 06 Jan 2017 15:45:33: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.broadPeak 
INFO  @ Fri, 06 Jan 2017 15:45:39: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign_peaks.gappedPeak 
INFO  @ Fri, 06 Jan 2017 15:45:43: Done!

Num	7
ID	task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_16
Name	naive_overlap_thresh
Thread	thread_Root
PID	24368

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:25:55
End	2017-01-07 04:27:08
Elapsed	00:01:12
Timeout	01:00:00
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Dependencies

 
# SYS command. line 61

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.PooledInRep1AndRep2.regionPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
23940 (process ID) old priority 0, new priority 10
Waiting for 58 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2265	2445	.	0	.	19.9429920025622	-1	3.18760654130545	90

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270467.1	2265	2445	.	0	.	19.9429920025622	-1	3.18760654130545	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2551	2731	.	0	.	11.5677656620501	-1	3.31844391275814	90

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270467.1	2551	2731	.	0	.	11.5677656620501	-1	3.31844391275814	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
KI270442.1	74358	74538	.	0	.	6.70219581790863	-1	2.30450925987837	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.regionPeak.gz has inconsistent naming convention for record:
KI270442.1	74358	74538	.	0	.	6.70219581790863	-1	2.30450925987837	90

Num	8
ID	task.callpeak_idr.idr2_rep1_pr.line_73.id_17
Name	idr2 rep1-pr
Thread	thread_Root
PID	24369

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:27:09
End	2017-01-07 04:28:23
Elapsed	00:01:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 75

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 77

 idr --samples /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr1/SRR1370889_1.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/pseudo_reps/rep1/pr2/SRR1370889_1.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --peak-list /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.unthresholded-peaks.txt --rank signal.value --soft-idr-threshold 0.05 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

 idr_thresh_transformed=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 84

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.13-col.bed.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz | grep -P 'chr[dXY]+[ 	]' | awk 'BEGIN{OFS="	"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.13-col.bed.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.13-col.bed.gz

# SYS command. line 97

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
24517 (process ID) old priority 0, new priority 10
Waiting for 36 seconds.

 
--------------------Stderr--------------------
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.53 1.46 0.88 0.12]
Number of reported peaks - 7080/7080 (100.0%)

Number of peaks passing IDR cutoff of 0.05 - 347/7080 (4.9%)

Num	9
ID	task.callpeak_idr.idr_final_qc.line_219.id_20
Name	idr final qc
Thread	thread_Root
PID	24370

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:28:24
End	2017-01-07 04:29:36
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.narrowPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/qc/ZNF669_IDR_final.qc
Dependencies

 
# SYS command. line 221

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 223

 echo -e "Nt\tN1	N2	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/qc/ZNF669_IDR_final.qc

# SYS command. line 224

 echo -e "0\t5	0	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/qc/ZNF669_IDR_final.qc

# SYS command. line 226

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
24666 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

Num	10
ID	task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_21
Name	blacklist_filter peak 1
Thread	thread_Root
PID	54215

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:29:38
End	2017-01-07 04:30:46
Elapsed	00:01:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
54221 (process ID) old priority 0, new priority 10
Waiting for 59 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3309	3489	.	0	.	32.3297592599516	-1	2.91539983521229	90

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/rep1/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz has inconsistent naming convention for record:
KI270467.1	3309	3489	.	0	.	32.3297592599516	-1	2.91539983521229	90

Num	11
ID	task.report.peak2hammock.line_412.id_22
Name	peak2hammock
Thread	thread_Root
PID	1366

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:30:47
End	2017-01-07 04:30:55
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock.gz
Dependencies

 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/spp/overlap/SRR1370889_1.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.tmp

   
--------------------Stdout--------------------
1370 (process ID) old priority 0, new priority 10

Num	12
ID	task.report.peak2hammock.line_412.id_23
Name	peak2hammock
Thread	thread_Root
PID	2010

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:30:56
End	2017-01-07 04:31:05
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/peak/idr/pseudo_reps/rep1/ZNF669_rep1-pr.IDR0.05.filt.12-col.bed.tmp

   
--------------------Stdout--------------------
2014 (process ID) old priority 0, new priority 10

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	2714

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-01-07 04:31:06
End	2017-01-07 04:31:14
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/report/ZNF669_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/report/ZNF669_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/report/ZNF669_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
2718 (process ID) old priority 0, new priority 10

Type	Name	Value
string	_	/usr/bin/bds
string	_LMFILES_	/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/ascp/3.5.6:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/homer/default
bool	allowEmpty	false
string[]	args	[-title, ZNF669, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/ZNF669/out, -bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669/out/align/rep1/SRR1370889_1.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/HughesInputData/input15MReadsNSCLess1.05.50MSubsample.tagAlign.gz, -final_stage, idr, $]
string	ASCPKEY	/software/ascp/etc/asperaweb_id_dsa.openssh
bool	canFail	false
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:10.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_veRoBQ
string	LANG	en_US.UTF-8
string	LOADEDMODULES	modsappsdir/modsappsdir:ascp/3.5.6:sratoolkit/2.5.2:homer/default
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESAPPSDIR	/software
string	MODULESHOME	/software/env_module/3.2.10
string	NLSPATH	/usr/dt/lib/nls/msg/%L/%N.cat
string	node
int	P	1125899906842624
string	PATH	/software/ucsc_tools/3.0.9:/software/weblogo/2.8.2:/software/homer/default/bin:/software/sratoolkit/2.5.2/bin/:/software/ascp/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect
string	PERL5LIB	/users/imk1/perl5/lib/perl5
string	PERL_LOCAL_LIB_ROOT	/users/imk1/perl5
string	PERL_MB_OPT	--install_base \"/users/imk1/perl5\"
string	PERL_MM_OPT	INSTALL_BASE=/users/imk1/perl5
real	PI	3.141592653589793
string	ppwd	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Najafabadi2015Data/hg38Mapping/ZNF669
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/
string	queue
int	retry	0
string	RULEFITBASE	/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/
string	SHELL	/bin/bash
string	SHLVL	3
string	SSH_CLIENT	171.65.77.8 43899 22
string	SSH_CONNECTION	171.65.77.8 43899 171.65.76.63 22
string	SSH_TTY	/dev/pts/0
string	STY	28209.ZNF669.BDS
string	system	sge
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:
int	timeout	-1
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1048
string	XDG_SESSION_ID	1080
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope